“Everything is everywhere – the environment selects.” (Baas-Becking, 1934)

“Although there is no direct effect of distance per se, distance is related to the likelihood that past divergence of biotic assemblages, whether due to genetic drift or adaptation to past environments, is maintained by genetic isolation.” (Hughes Martiny et al., 2006)

Why should microbes be universal?

• Small• Abundant• Metabolically plastic• Can remain dormant for long times (“seedbank”)

• Some nearly identical 16S rRNA from each polar ocean (Massana et al., 2000)

• Universal dispersal, differential growth…

Biogeography compared to macrofauna

• Darwin’s “three great facts”

• Are microbes cosmopolitan? Endemic?– Variation amongst microbes– What forces lead to geographically structured

populations?

Biogeography compared to macrofauna

• Darwin’s “three great facts”

• Are microbes cosmopolitan? Endemic?– Variation amongst microbes– What forces lead to geographically structured

populations?

(Johnson et al., 2006)

Diversity vs. distance

• BOX-PCR of fluorescent Pseudomonas isolates taken from 4 continents (Cho & Tiedje, 2000)

Diversity vs. distance

(Hughes Martiny et al., 2006)

• BOX-PCR of fluorescent Pseudomonas isolates taken from 4 continents (Cho & Tiedje, 2000)

• Positive local correlation, negative global correlation

Non-random distributions of free-living taxa

(Hughes Martiny et al., 2006)

Why do organisms live where they do?

• Contemporary environment vs. historical events?– Is it really geography, or

simply niche differences?

• Why would geography matter?– Constraints on dispersal and

colonization– Diversification and extinction

(Hughes Martiny et al., 2006)

Biogeography: flagellates

• Diversity of Paraphysomonas

(Finlay, 2002)(Finlay & Clarke, 1999)

Biogeography: Sulfolobus

• Sequenced 9 loci from 78 isolates from hot springs (Whitaker et al., 2003)

– Group by geography– No significant correlation

with pH or temperature

Biogeography: phage• Exchange due to recombination or reassortment

during coinfections– Isolated and sequenced cystoviridae from Pseudomonas

syringae pathovar phaseolicola (Silander et al., 2005)

Microbes in a host w/ biogeography: Helicobacter pylori

• Sequenced 8 loci from 370 isolates from 27 geographical, ethnic and/or linguistic groupings (Falush et al., 2003)

– 1418 polymorphic nt positions

Microbes in a host w/ biogeography: Helicobacter pylori

• STRUCTURE - deduces populations from MLST – Define populations (Fig. 1A) & subpopulations (1B)

• Assumes linkage equilibrium, association much less globally than within defined populations (4-5 sufficient)

• Disequilibrium due to very short stretches (r = 0.0296, thus average chunk of 34 bp)

Microbes in a host w/ biogeography: Helicobacter pylori

• STRUCTURE - deduces populations from MLST – Define ancestry (Fig. 1C)

• Optimal number of past groups to achieve current mixture

Maori Inuit

white South African England

Microbes in a host w/ biogeography: Helicobacter pylori

• Global picture of present and past

• Coherence between host and microbe– We have imposed a

geographic structure

Evolutionary history of Salmonella typhi

• Very little diversity (2 nt amongst 3.3 kb from 26 isolates) – is it all a new sweep?

• ‘Mutation discovery’ of 199 gene fragments (~500 bp) from 105 strains = 88.7 kb (Roumagnac et al., 2006)

– 66 were polymorphic– 37 non-synonomous to 33 synonomous

• Only weak bias in Ka/Ks for housekeeping vs. cell surface

– 5 look like HGT• Two ~25 kb regions from

S. enterica serovar Typhimurium• One gene with 6 SNPs from

S. enterica serovar Paratyphi A

Evolutionary history of Salmonella typhi

• MLST data to generate minimal spanning tree

• Highly unusual– 100% parsimonious– 3 hypothetical nodes– Ancestral node present

• H45 has ancestral seq. for every locus

– Branches largely 1 SNP• Long persistence, present

on multiple continents

Evolutionary history of Salmonella typhi

• Estimate tmrca using two estimates of clock– 10-43 kya or 26-71 kya

• Effective population size (Ne) currently 2.3 x 105 – 1.0 x 106

Evolutionary history of Salmonella typhi

• Screened 55 loci for 59 older strains (1958-1967) from Africa and Vietnam– Found ancestral nodes– Persistent

Evolutionary history of Salmonella typhi

• Response to new selective pressure: NalR

– First used in SE Asia in 1989 (NalR found in 1991)– Screened an additional 295 strains from SE Asia

No fixation…

Genetic parallelism

2.5 x 108 higher rate of mutation than long-term